Biology Commons^™

The Acidic Domains Of The Toc159 Chloroplast Preprotein Receptor Family Are Instrinsically Disordered Protein Domains, Lynn G.L. Richardson, Masoud Jelokhani-Niaraki, Matthew D. Smith

Biology Faculty Publications

Background: The Toc159 family of proteins serve as receptors for chloroplast-destined preproteins. They directly bind to transit peptides, and exhibit preprotein substrate selectivity conferred by an unknown mechanism. The Toc159 receptors each include three domains: C-terminal membrane, central GTPase, and N-terminal acidic (A-) domains. Although the function(s) of the A-domain remains largely unknown, the amino acid sequences are most variable within these domains, suggesting they may contribute to the functional specificity of the receptors.

Results: The physicochemical properties of the A-domains are characteristic of intrinsically disordered proteins (IDPs). Using CD spectroscopy we show that the A-domains of two Arabidopsis Toc159 …

Mir319a Targeting Of Tcp4 Is Critical For Petal Growth And Development In Arabidopsis, Anwesha Nag, Stacey King, Thomas Jack

Dartmouth Scholarship

In a genetic screen in a drnl-2 background, we isolated a loss-of-function allele in miR319a (miR319a¹²⁹). Previously, miR319a has been postulated to play a role in leaf development based on the dramatic curled-leaf phenotype of plants that ectopically express miR319a (jaw-D). miR319a¹²⁹ mutants exhibit defects in petal and stamen development; petals are narrow and short, and stamens exhibit defects in anther development. The miR319a¹²⁹ loss-of-function allele contains a single-base change in the middle of the encoded miRNA, which reduces the ability of miR319a to recognize targets. Analysis of the expression patterns of the …

Effects Of Temperature On Gene Expression In Embryos Of The Coral Montastraea Faveolata, Christian Voolstra, Julia Schnetzer, Leonid Peshkin, Carly J. Randall, Alina M. Szmant, Mónica Medina

Biomedical Engineering and Sciences Faculty Publications

Coral reefs are expected to be severely impacted by rising seawater temperatures associated with climate change. This study used cDNA microarrays to investigate transcriptional effects of thermal stress in embryos of the coral Montastraea faveolata. Embryos were exposed to 27.5°C, 29.0°C, and 31.5°C directly after fertilization. Differences in gene expression were measured after 12 and 48 hours.Results: Analysis of differentially expressed genes indicated that increased temperatures may lead to oxidative stress, apoptosis, and a structural reconfiguration of the cytoskeletal network. Metabolic processes were downregulated, and the action of histones and zinc finger-containing proteins may have played a role in the …

Defining The Role Of Syndecan-4 In Mechanotransduction Using Surfacemodification Approaches, Robert M. Bellin, James D. Kubicek, Matthew J. Frigault, Andrew J. Kamien, Robert L. Steward, Hillary M. Barnes, Michael B. Digiacomo, Luke J. Duncan, Christina K. Edgerly, Elizabeth M. Morse, Chan Young Park, Jeffrey J. Fredberg, Chao Min Cheng, Philip R. Leduc

Biology Department Faculty Scholarship

The ability of cells to respond to external mechanical stimulation is a complex and robust process involving a diversity of molecular interactions. Although mechanotransduction has been heavily studied, many questions remain regarding the link between physical stimulation and biochemical response. Of significant interest has been the contribution of the transmembrane proteins involved, and integrins in particular, because of their connectivity to both the extracellular matrix and the cytoskeleton. Here, we demonstrate the existence of a mechanically based initiation molecule, syndecan-4. We first demonstrate the ability of syndecan-4 molecules to support cell attachment and spreading without the direct extracellular binding of …

Inferring Dispersal Of Aquatic Invertebrates From Genetic Variation: A Comparative Study Of An Amphipod (Talitridae Hyalella Azteca) And Mayfly (Baetidae Callibaetis Americanus) In Great Basin Springs, Heather Lynn Stutz

Theses and Dissertations

Whether active or passive, dispersal accompanied by gene flow shapes the population genetics and evolutionary divergence of species. Indirect methods which use genetic markers have the ability to assess effective dispersal—that which resulted in gene flow. My objective was to see if an aquatic insect and an obligate aquatic invertebrate show similar phylogeographic patterns and genetic uniqueness. Hyalella azteca and Callibaetis americanus were collected from 4-5 springs in each of six basins in the Great Basin of western North America. No dispersal or genetic studies of C. americanus have been conducted to date. However, several studies focusing on mtDNA diversity …

Environmental Dna Sequencing Primers For Eutardigrades And Bdelloid Rotifers, Byron J. Adams, Jeremy Whiting, Elizabeth K. Costello, Kristen R. Freeman, Andrew P. Martin, Michael S. Robeson, Steve K. Schmidt

Faculty Publications

Background: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms. Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly …

The Ecological Importance Of Extrinsic And Intrinsic Drivers Of Animal Movement, Josh Earl Rasmussen

Theses and Dissertations

The movement of individuals is foundational to many ecological processes. For example, the movement of an organism from one place to another alters population density at both sites and has potential for affecting the genetic dynamics within the new population. Individual movement events may be in synchrony with overall trends in populations, e.g. spawning migrations, or may be atypical (asynchronous). This latter movement type can affect population and metapopulation dynamics, depending on its prevalence within a population. Nevertheless, given the complexity of interactions, the causative factors of movement are understood vaguely, much less for aquatic organisms. Drivers of movement are …

Zooplankton Abundance, Community Composition And Grazing In The James River Estuary (Virginia, Usa), Laura E. Barry

Theses and Dissertations

This study examined the extent to which zooplankton in the James River Estuary (Virginia, USA) exploit the available algal-food resources. Zooplankton abundance, community composition and grazing rates were assessed at three locations which included a site with high algal production (near the VCU Rice Center) and two sites where algal production was lower. Grazing rates were measured by determining the rate of phytoplankton decline (as chlorophyll a) during 48-hour incubation experiments in the presence and absence of zooplankton. Significant differences in zooplankton abundance were observed among the three sites, with the greatest average zooplankton density (434 ± 69 ind/L) occurring …

Examining The Effects Of Penning On Juvenile Eastern Box Turtles (Terrapene Carolina Carolina), Nicolas Frederick

Theses and Dissertations

Box turtle (Terrapene carolina) populations have been declining over the last several decades, and one major cause is increasing urbanization. As a result of habitat fragmentation, wildlife managers are frequently turning to new and alternative management strategies. Traditional box turtle management has included relocation, which has been met with limited success. This study aims to combine these strategies with another less-studied one: forcing turtles to overwinter on site by penning them in an outdoor enclosure. Two sets of juvenile box turtles were released at the Virginia Commonwealth University Rice Center: one penned on site in a pen for one year, …

Distribution And Diversity Of Archaeal And Bacterial Ammonia Oxidizers In Salt Marsh Sediments, Nicole S. Moin, Katelyn A. Nelson, Alexander Bush, Anne E. Bernhard

Biology Faculty Publications

Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP were equally distributed between the water column/sediment and soil/sediment clades, while AOA amoA sequences at SAS were primarily affiliated with the …

Phylogeography And Postglacial Dispersal Of Smallmouth Bass (Micropterus Dolomieu) Into The Great Lakes, W. Calvin Borden, Robert A. Krebs

Biological, Geological, and Environmental Faculty Publications

Refugia and dispersal routes of smallmouth bass (Micropterus dolomieu) into the Great Lakes were identified using 427 mitochondrial sequences from across their native range. Overall, smallmouth bass accessed the Great Lakes via long-distance dispersal from multiple refugia, and the distribution of genetic variation reflected the consequences of vicariant, dispersal, and paleogeological events. Proximity of lakes to glacial outlets had a greater predictive power on the resulting distribution of mitochondrial diversity relative to interbasin migration. Populations in the Eastern and Interior Highlands contained the most divergent and oldest haplotypes, reflecting their role as glacial refugia and subsequent high incidence of endemicity. …

Remodeling Of The Tight Junction During Recovery From Exposure To Hydrogen Peroxide In Kidney Epithelial Cells, Jeannette E. Gonzalez, R. J. Digeronimo, D'Ann E. Arthur, Jonathan M. King

Biology Faculty Research

Renal ischemia-reperfusion injury results in oxidative stress-induced alterations in barrier function. Activation of the mitogen-activated protein (MAP) kinase pathway during recovery from oxidative stress may be an effector of oxidant-induced tight junction reorganization. We hypothesized that tight junction composition and barrier function would be perturbed during recovery from oxidative stress. We developed a model of short-term H₂O₂ exposure followed by recovery using Madin Darby canine kidney (MDCK II) cells. H₂O₂ perturbs barrier function without a significant cytotoxic effect except in significant doses. ERK-1/2 and p38, both enzymes of the MAP kinase pathway, were activated …

Remote Sensing Of Harmful Algal Blooms In The Mississippi Sound And Mobile Bay: Modelling And Algorithm Formation, Dan Martin Holiday

Dissertations

The incidence and severity of harmful algal blooms have increased in recent decades, as have the economic effects of their occurrence./The diatom Pseudo-nitzschia spp. caused fisheries closures in Mobile Bay during 2005 due to elevated levels of domoic acid. In the previous 4 years Karenia brevis counts of >5,000 cells L"1 have occurred in Mobile Bay and the Mississippi Sound. Population levels of this magnitude had previously been recorded only in 1996. Increases in human populations, urban sprawl, development of shoreline properties, sewage effluent and resultant changes in NP ratios of discharge waters, and decline in forest and marsh lands, …

First Record Of The Extinct Sawfish Propristis Schweinfurthi Dames, 1883 (Batoidea: Pristiformes: Pristidae) From The Middle Eocene Of Spain, Francesc Farrés, Harry L. Fierstine

Biological Sciences

A partial rostrum of Propristis schweinfurthi Dames, 1883 was collected in the Bartonian strata of northeastern Spain. The specimen represents the second record of the species from Europe, and the second occurrence of a sawfish (Mesopristis osonensis Farrés, 2003) from the Vic-Manlleu Marls Formation. In spite of some evidence to the contrary, Propristis probably preferred ecological conditions similar to extant sawfishes, i.e., inhabiting near shore tropical to subtropical seas with occasional excursions into freshwater.

The Effects Of A Reservoir On Genetic Isolation In Two Species Of Darters, Kerstin Lindsay Edberg

Masters Theses & Specialist Projects

The addition of dams into a riverine system causes a wide range of changes (i.e., sedimentation, erosion, thermal) to the river as well as to the fish assemblages of that river. Although there have been many studies documenting the changes that occur to the fish assemblages in the impounded river, there have been fewer studies examining the effects of a reservoir on the fish inhabiting the tributaries upstream of the impoundment. One possible impact of a reservoir could be to act as a barrier to fish migration between streams.
To determine if reservoirs restrict migration, the genetic diversity of two …

A New North American Genus Of Hetaeraiinae (Coleoptera: Histeridae), With Descriptions Of Six New Species From The U.S.A. And Mexico, Michael S. Caterino, Alexey K. Tishechkin

Publications

Renclasea n. gen., a genus of the Hetaeriinae (Histeridae), with six species, R. skelleyi n. sp. (United States: Florida and Georgia), R. falli n. sp. (United States: California), R. helavai n. sp. (United States: Arizona), R. mexicana n. sp. (Mexico: Hidalgo), R. occidentalis n. sp. (United States: Arizona and New Mexico) and R. cazieri n. sp. (United States: Arizona), are described, illustrated and diagnosed. The status of two female specimens of Renclasea from western Texas, apparently closely related to R. occidentalis, remains uncertain. The only host record available for the genus is an association of R. mexicana with undetermined species …

Introducing Mothur: Open-Source, Platform-Independent, Community-Supported Software For Describing And Comparing Microbial Communities, Courtney Robinson

Department of Biology Faculty Publications

mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

The Behavioral And Pharmacological Actions Of Nmda Receptor Antagonism Are Conserved In Zebrafish Larvae, John Chen, Roshni Patel, Theodore Friedman, Kevin Jones

Department of Biology Faculty Publications

Dizocilpine maleate (MK-801) is one of several NMDA receptor antagonists that is widely used to pharmacologically model the symptoms of psychosis and schizophrenia in animals. MK-801 elicits behaviors in adult zebrafish (Danio rerio) that are phenotypically consistent with behaviors observed in humans and rodents exposed to tbhe drug. However, the molecular and cellular processes that mediate the psychotomimetic, cognitive and locomotive behaviors of MK-801 are unclear. We exposed zebrafish larvae to MK-801 to assess their merit as a model organism to elucidate the behavioral effects of NMDA receptor blockade. Zebrafish larvae were acutely immersed in MK-801 to assess the effect …

Applications Of Natural Products In The Control Of Mosquito-Transmitted Diseases, Jesse Hardin, Fatimah Linda Collier Jackson

Department of Biology Faculty Publications

Mosquito-transmitted diseases remain one of the most significant causes of mortality in the African continent, despite successes in controlling these diseases in other regions of the world. The disproportionate impact in areas of poverty suggests a need for control that is efficient and does not require complex technological control strategies. Focusing on the vectors of disease, the mosquito, there are many alternatives to synthetic, chemical pesticides that await discovery and development. Although some natural products have been described, there is still a need for continuing research that incorporates endogenous knowledge in the selection process for potential vector control candidates. Recent …

Dissolved Organic Matter Influences The Timing Of Embryonic Development Of The Purple Sea Urchin, Strongylocentrotus Purpuratus., Corbin J. Hodges

Master's Theses

Marine dissolved organic matter (DOM) comprises one of the largest carbon reservoirs on earth and has long been considered a potential energy source for marine invertebrates. The importance of DOM transport has been adequately demonstrated for unicellular organisms, where DOM can meet 100% of an organisms energy needs, but the effects of DOM uptake for marine metazoans are less well understood. In this study, three general areas involving the influence of DOM transport to marine invertebrates were explored. First, we assessed the effects of using seawater exposed to high intensity ultraviolet radiation (UVR) on the study organism; embryos of the …

The Effect Of Plant Source Location On Restoration Success: A Reciprocal Transplant Experiment With Winterfat (Krascheninnikovia Lanata), Melanie G. Barnes

Biology ETDs

It is increasingly important that plant propagules used in revegetation projects are from a location that is geographically or ecologically similar to the planting site. To better understand the consequences of using non-local plant materials, I chose to study the population biology of the widespread shrub winterfat (Krascheninnikovia lanata, Chenopodiaceae) among five populations in New Mexico, USA. Winterfat plant morphology among the five populations was compared, and the rate of emergence and floral onset was measured in a greenhouse common garden. A reciprocal transplant experiment was planted in which individuals from different locations were planted in replicate common gardens. Transplant …

The Role Of Spatial And Genetic Modeling To Biogeography, Dolly Lyne Crawford

Biology ETDs

One of the most persistent challenges in biology is explaining the distribution of animal taxa. Quantitative explanations for the distribution of organisms are challenged by the complexity of factors that potentially limit a species range, including topography, ecology, climate and biology. Because of limits on data and approaches, early biogeographers were hampered in their ability to explain patterns. Here, I benefit from two primary developments in biogeography. My research draws from the accumulation of data across several scientific disciplines and advances in spatial and statistical approaches to examine the distribution of animal taxa within an integrative biogeography framework. I combine …

The Physiological Ecology And Evolution Of Freezing Tolerance In Diploid Larrea Sp., Juliana Sibylla Medeiros

Biology ETDs

A basic understanding of vegetation responses to temperature and precipitation variability is paramount to the understanding of ecological adaptation, and comparisons across warm deserts are needed to increase our understanding of the controls on establishment in warm desert ecosystems. At the high latitude edges of warm deserts drought and freezing lower plant performance due to xylem dysfunction, as freeze-thaw embolism reduces stomatal conductance, or damage to leaf photosynthetic apparatus, as tissue desiccation reduces photosynthetic efficiency. Variation in these physiological responses can be observed across life-history stages, genetic background, climate gradients, and species, and this variation may be acted on by …

Statistical Methods In Microarrays And High-Throughput Flow Cytometry, Osorio Meirelles

Biology ETDs

Abstract-I

Background: Heterogeneous cell populations have previously been described as noisy. However, recent studies have demonstrated that heterogeneity can be biologically significant. We present here an approach for rapid and complete identification of heterogeneous cell populations from high-throughput flow cytometry data. We have developed a novel measure Slope Differentiation Identification (SDI) using flow cytometry-based protein expression, quantifying the rate of change in protein expression between two conditions (exponential and stationary phase) of yeast cells, as a function of cell size or cell granularity.

Results: SDI had superior Gene Ontology enrichment when compared with other approaches such as k-means clustering and …

The Ecology Of The Peaks Of Otter Salamander (Plethodon Hubrichti) In Sympatry With The Eastern Red-Backed Salamander (Plethodon Cinereus), Norman Reichenbach, Andrew Kniowski

Faculty Publications and Presentations

The Peaks of Otter Salamander, Plethodon hubrichti, is found along a 19 km length of the Blue Ridge Mountains, Virginia, USA, often in sympatry with the Eastern Red-backed Salamander, P. cinereus. In a sympatric area of Bedford County, Virginia, we conducted a mark-recapture study on a 10 × 10 m site. Surface densities of salamanders increased as the number of days without precipitation prior to a collection event increased. This suggests vertical movements in response to surface moisture. When salamanders returned to the surface after rain, individuals appeared to “shuffle” between rocks and likely, leaf litter. That is, we were …

Don't Diss Integration: A Comment On Ricklefs's Disintegrating Communities, Rob W. Booker, Ragan M. Callaway, Lohengrin A. Cavieres, Zaal Kikvidze, Christopher J. Lortie, Richard Michalet, Francisco I. Pugnaire, Alfonso Valiente-Banuet, Thomas G. Whitham

Biological Sciences Faculty Publications

No abstract provided.

Remarks On The Stability Of Some Size-Structured Population Models Vi: The Case When The Death Rate Depends On Juveniles Only And The Growth Rate Depends On Size Only And The Case When Both Rates Depend On Size Only, M. El-Doma

Applications and Applied Mathematics: An International Journal (AAM)

We continue our study of size-structured population dynamics models when the population is divided into adults and juveniles, started in El-Doma (to appear 1) and continued in El-Doma (to appear 2). We concentrate our efforts in two special cases, the first is when the death rate depends on juveniles only and the growth rate depends on size only, and, the second is when both the death rate and the growth rate depend on size only. In both special cases we assume that the maximum size for an individual in the population is infinite. We identify three demographic parameters and show …

Drosophila Adult Eye Model To Teach Scanning Electron Microscopy In An Undergraduate Cell Biology Laboratory, Meghana Tare, Oorvashi Roy Puli, Sarah M. Oros, Amit Singh

Biology Faculty Publications

We have devised an undergraduate laboratory exercise to study tissue morphology using fruit fly, Drosophila melanogaster, as the model organism. Drosophila can be reared in a cost effective manner in a short period of time. This experiment was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of scanning electron microscopy (SEM) technique to study the morphology of adult eye of Drosophila. The adult eye of Drosophila is a compound eye, which comprises of 800 unit eyes, and serves as an excellent model for SEM studies. We used flies that …

Remarks On The Stability Of Some Size-Structured Population Models V: The Case When The Death Rate Depends On Adults Only And The Growth Rate Depends On Size Only, M. El-Doma

Applications and Applied Mathematics: An International Journal (AAM)

We continue our study of size-structured population dynamics models when the population is divided into adults and juveniles, started in El-Doma (To appear). We concentrate our efforts in the special case when the death rate depends on adults only, the growth rate depends on size only and the maximum size for an individual in the population is infinite. Three demographic parameters are identified and are shown to determine conditions for the (in)stability of a nontrivial steady state. We also give examples that illustrate the stability results. The results in this paper generalize previous results, for example, see Calsina, et al. …

Pulsatile Flow Of Blood In A Constricted Artery With Body Acceleration, Devajyoti Biswas, Uday Shankar Chakraborty

Applications and Applied Mathematics: An International Journal (AAM)

Pulsatile flow of blood through a uniform artery in the presence of a mild stenosis has been investigated in this paper. Blood has been represented by a Newtonian fluid. This model has been used to study the influence of body acceleration and a velocity slip at wall, in blood flow through stenosed arteries. By employing a perturbation analysis, analytic expressions for the velocity profile, flow rate, wall shear stress and effective viscosity, are derived. The variations of flow variables with different parameters are shown diagrammatically and discussed. It is noticed that velocity and flow rate increase but effective viscosity decreases, …